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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tilingArray_1.91.0.tar.gz','quit-with-status'=TRUE)"
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── Installing tilingArray ──────────────────────────────────────────────────────
✔ Package installed successfully
── tilingArray session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp62bBop/file14cabc6b4a825d/tilingArray
→ BiocVersion: 3.24
→ Package: tilingArray
→ PackageVersion: 1.91.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/tilingArray.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp62bBop/file14cabc6b4a825d/tilingArray
→ installDir: /tmp/Rtmp62bBop/file14cabc5616d6c8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tilingArray ────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 2.11.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • assessNorm.Rnw
    • ...
    • segmentation.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/plotAlongChrom.Rnw (chunk no. 6, line 60, column 85)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/assessNorm.Rnw
    • ...
    • vignettes/segmentation.Rnw
* Checking package installation calls in R code...
* Checking for library/require of tilingArray...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotAlongChrom.R (line 496, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • comparisonPlot.R (line 11, column 12)
    • ...
    • segChrom.R (line 1, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/findsegments.R (line 16, column 5)
    • ...
    • cat() in R/segChrom.R (line 82, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 9, column 19)
    • ...
    • R/segChrom.R (line 74, column 22)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotAlongChrom.R (line 69, column 10)
    • R/plotSegmentationDots.R (line 60, column 12)
    • R/plotSegmentationHeatmap.R (line 38, column 12)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/qcPlots.R (line 11, column 5)
    • system() in R/segChrom.R (line 25, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/gffSub.Rd
ℹ Found @ in man/plotAlongChrom.Rd
ℹ Found @ in man/plotSegmentationHeatmap.Rd
ℹ Found @ in man/segnf.Rd
ℹ Found @ in vignettes/findsegments.Rnw
ℹ Found @ in vignettes/plotAlongChrom.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • plotAlongChrom() (R/plotAlongChrom.R): 274 lines
    • ...
    • plotSegmentationHeatmap() (R/plotSegmentationHeatmap.R): 92 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gffSub.Rd
    • ...
    • man/segnf.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • breakpointsPretend.Rd
    • ...
    • segChrom.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • readCel2eSet.Rd
    • segChrom.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • readCel2eSet.Rd
    • segChrom.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 275 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L11 ## check that slots 'breakpoints', 'lo ...
    • ...
    • vignettes/plotAlongChrom.Rnw#L171 Along-chromosome raster heatmap plot of
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 51 lines (1%) contain tabs.
  First few lines:
    • R/plotAlongChrom.R#L111 # for case 2 or 3. ...
    • ...
    • man/segnf.Rd#L24 gff=gffSub,rowNamesHeatmap=nmLabel) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1418 lines (40%) are
not.
  First few lines:
    • R/AllClasses.R#L11 ## check that slots 'breakpoints', 'lo ...
    • ...
    • vignettes/plotAlongChrom.Rnw#L167 colHeatmap = colorRamp(brewer.p ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 20 NOTES
ℹ See the tilingArray.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.